When the 5 richest and most powerful girls at an exclusive private high school are sent a death threat they decide to take matters into their own hands and bring divine retribution to their would be assailants. Using their collective resources and skills they show the terrorists that they messed with the wrong girls.

Following the Little Busters after they lost their first baseball game, the team decides to have a pancake party. It has been almost one semester since the return of Kyousuke Natsume. As usual, Riki Naoe continues to help the Little Busters' members—both old and new—with confronting their inner struggles. However, strange happenings begin to occur, leading Rin Natsume and Riki closer to unraveling the truth behind the "secret of this world."

Little do Rin and Rikki know, their discovery will end up changing the peaceful everyday lives created by the Little Busters once and for all. Little Busters!: Refrain brings a conclusion to the colorful stories of its ensemble cast—forged with the weight of emotions and strengthened with the bond of friendship—as they come to terms with their regrets and weaknesses.

Riki was a child when his parents died, leaving him hopeless and depressed. What saved him was a group of four kids calling themselves the Little Busters. They took Riki out and played with him during his time of need. He really enjoyed being together with them, and his grief gradually faded away. Now in his second year of high school they still hang out, fight and live together, and enjoy their school life.